Wheat stripe rust, caused by basidiomycete fungus Puccinia striiformis f. sp. tritici (Pst), is a damaging disease worldwide. The recent discovery demonstrated the fungus depends on living wheat and aecial hosts, mainly barberry (Berberis) species, to complete its life cycle. In China, we determined that, under natural conditions, the sexual cycle of Pst occurs based on collections of Pst isolates from the diseased barberry in the past three years. However, no direct evidence to support whether barberry plays a role in spreading inoculums to wheat field to cause stripe rust was detected. In the present study, we recovered 103 Pst samples from natural-infected B. shensiana in the western Shaanxi in spring 2016, and also collected 107 Pst isolates from neighboring wheat fields. Phenotype and genotype of the two Pst populations were tested using a set of Chinese differential hosts for Pst and SSR markers, respectively. The phenotype tests showed that 57 race types produced from the barberry-derived Pst populations, consisting of 58 known races, such as CYR 34, CYR32, G22-14, and Su11-14-3, and 45 new races. Many of the two Pst populations shared the same race types. The genotype tests indicated the barberry-derived Pst population produced a rich genotype, obviously higher than the wheat-derived Pst populations. The seven same genotypes were found on 40 isolates of the former and 26 of the latter. Our results provide evidence to support that sexual cycle of Pst occurs regularly in nature in China and that barberry provides inoculums to neighboring wheat fields, triggering stripe rust infections in the spring. This could be a reason why the Chinese Pst populations represent extreme genetic diversity.

Pathogens, whatever their types, develop at the expense of the nutrients generated by host and it is largely assumed that classical sources turn into sinks when colonized by pathogens. Sugar appears to be the major carbon and energy source transferred from the host to pathogens. Uptake, exchanges and competition for sugar, at biotrophic interfaces, are controlled by membrane transporters and their regulation patterns are essential in determining the outcome of plant-fungal interactions. However, mechanisms of transport and transporters involved in carbon partitioning between organisms are still poorly understood.
In this study, a wheat sugar transporter protein (STP) gene, TaSTP1, was cloned from a wheat-Puccinia striiformis f. sp. tritici (Pst) interaction cDNA library. Transcripts of TaSTP1 were up-regulated in wheat leaves that were infected by Pst or had experienced exogenous ABA and certain abiotic treatments. Heterologous mutant complementation in Saccharomyces cerevisiae revealed that TaSTP1 transports a broad-spectrum monosaccharides including glucose, fructose, mannose and galactose. Transient expression in Nicotiana benthamiana and Arabidopsis protoplasts suggested that TaSTP1 is localized in plasma membrane. Yeast two hybrid and bimolecular fluorescence complementation (BiFC) validated oligomerization of TaSTP1. Knocking down TaSTP1 using the barley stripe mosaic virus-induced gene silencing system reduced the susceptibility of wheat to the Pst virulent pathotype CYR31. Hyphal abnormality was significantly observed in VIGS plants. These results suggest that TaSTP1 may directly or indirectly participate in sugar transport in the wheat-Pst interactions and exert influence on suagr supply of Pst.

Stripe rust, caused by Puccinia striiformis tritici (Pst), continues its evolution towards virulence to race-specific resistance genes. Identification of Mexican Pst isolates MEX16-03 and MEX16.04 that changed infection types of Yr10 testers from 1 to 9 and for Yr24 (=Yr26) testers from 3 to 9 indicated that a mutation for virulence to these resistance genes has occurred in a predominant race detected in 2014 and maintained at CIMMYT as MEX14.191 and at INIFAP as CMEX14.25. Isolate MEX14.191 was responsible for the susceptibility of popular varieties Nana F2007 and Luminaria F2014 grown in central Mexican highlands. Isolate MEX16.04 has the following avirulence/virulence formula: Yr1, 5, 15, SP/Yr2, 3, 6, 7, 8, 9, 10, (17), 24, 26, 27, 28, 31, 32 using the Avocet near-isolines and other known testers. Virulence to Yr10 and Yr24 (=Yr26) were also confirmed by testing seedlings of cultivars Moro (Yr10), Chuanmai 42, and Neimai 836 (Yr24). Seedling tests carried on 200 bread wheat, 550 durum, and 460 synthetic hexaploid wheats with their respective durum parents from CIMMYT collection indicated that MEX16.03 and MEX16.04 do not represent a major threat because a majority of the lines remained resistant to these isolates. However, it is worth mentioning that durum cultivars, such as Khofa, Desert King, Anatoly, Movas, and Llareta INIA, and 10 primary synthetic hexaploid or synthetic-derived bread wheats that were resistant to MEX14.191 became susceptible to MEX16.03 and MEX16.04. Our results indicate that resistance gene Yr10 was absent and Yr24 occurred in low frequency in CIMMYT bread wheat germplasm. A majority of CIMMYT durum wheat possibly carried Yr24 in combination with other effective gene(s).

Wheat is one of the most important staple food and agricultural crop cultivated worldwide. To meet the demands of the raising human population, global wheat production has to be increased which is however declined due to appearance of highly virulent strains of Puccinia striiformis f. sp. tritici (Pst) fungus causing stripe rust disease. Globally, the incidence of stripe rust is effectively managed through the deployment of host plant mediated genetic resistance. But as the resistance present in the current wheat cultivars are ineffective, new sources of resistance particularly from pathogen unexposed genetic resources are of urgent need to prevent stripe rust epidemics. Landrace collections with rich genetic diversity and being less exposed to prevalent pathogen are of valuable source for resistance to new pathogens. In this study, a total of 295 landrace accessions collected by the famous Russian botanist Vavilov was screened for stripe rust resistance using the two predominant lineage Pst strains of Australia. Six accessions with good resistance against the two aggressive Pst strains were selected for genetic characterization and for utilization in global wheat breeding. Characterisation of these novel resistance were undertaken using combination of conventional and advanced genetic tools. While the conventional approach involves the traditional map based gene cloning, the other tool is the recently identified rapid method based on mutagenesis, targeted gene capture and next generation sequencing called "MutRenSeq". Subsequently, the identified novel resistant traits were transferred into elite wheat cultivars through the combination of linked molecular markers and speed breeding techniques. Thus along with the identification of novel resistance, elite wheat cultivars with broad spectrum stripe rust resistance were also generated through the use state of art techniques to sustain global wheat production from the rapidly evolving stripe pathogens.

The Ethiopian plateau hosts thousands of durum wheat landraces cultivated in low input agriculture conducted by an estimated 70 million smallholder farmers. Having thoroughly characterized the phenotypic and molecular uniqueness of Ethiopian durum wheat landraces, we produced a large nested association mapping (NAM) population harnessing their mostly untapped diversity in a set of recombinant inbred lines (RIL). The NAM founders are 50 landraces providing valuable traits such as drought tolerance and resistance to pests, and maximizing molecular diversity. Each selected landrace was crossed to a durum wheat line with an international background (Asassa), establishing independent interconnected bi-parental families, for a total of 6,280 RILs currently in F8. The Ethiopian NAM is at once i) a powerful QTL mapping tool that will side the increasing availability of genomic tools in wheat towards high-throughput candidate genes identification, and ii) a large pre-breeding panel closing the gap between local and international materials. Here we discuss the molecular and phenotypic characterization of twelve NAM families, represented by 100 RILs each. The 1,200 NAM RIL showed elevated allelic variation and a genetic structure reminiscent of the breeding design followed. The NAM RILs were phenotyped for ten agronomic and five disease traits in multiple locations in the Ethiopian highlands. A quantitative method eliciting smallholder farmers traditional knowledge was used to record local farmers appreciation of NAM RILs in all phenotyping locations. We report that the superior genetic properties of the NAM can be used to map QTL for both agronomic and farmer traits with unprecedented precision. The most promising NAM RILs can be identified combining farmers appreciation and agronomic measures, and prioritized for introgression of Ethiopian landraces traits in breeding pipelines aiming at higher uptake and productivity in local agriculture.

A diverse set of winter wheat germplasm was screened for resistance to stem rust in large-scale trials in Kenya and Turkey during 2009-16. The study aimed to select resistant material and characterize types of resistance and possible genes, as well as evaluate agronomic traits and resistance to other diseases to select superior variety candidates and parental lines. The study material was comprised of various Facultative and Winter Wheat Observation Nurseries (FAWWON), which are developed and distributed by the International Winter Wheat Improvement Program (www.iwwip.org) in Turkey. More than 1600 global accessions were screened, with most evaluated for two years. Based on stem rust data from Kenya, more than 400 genotypes were identified exhibiting adequate levels of resistance to the Ug99 race group. The highest number of resistant lines originated from IWWIP (~170), USA (~100), Russia (~40), Iran (~30), Romania (~20), and South Africa (~20). Material was also tested at two sites in Turkey: Haymana (artificial inoculation) and Kastamonu (natural infection). There was no significant correlation between stem rust severities in Kenya and in Turkey, due to differences in stem rust pathotypes. However, a set of germplasm (more than 100 entries) has been identified as resistant in both countries. This set represents promising material as variety candidates and parental lines; another study is currently identifying the genes controlling the stem rust resistance in this population. IWWIP distributed stem rust resistant germplasm to its global collaborators during 2010-2015, in response to the threat from the Ug99 race group. New resistant germplasm combining broad adaptation, high yields, and resistance to other diseases is available on request.

The Global Wheat Program of CIMMYT is one of the largest public breeding programs in the world consisting of millions of lines/ genotypes derived from thousands of crosses evaluated under using a shuttle breeding cycle and multi-environment testing. The germplasm is phenotyped for conventional (such as yield and grain quality) as well as non-conventional traits (physiological traits) in field and greenhouse conditions. The breeding germplasm is also screened with genome-wide markers (using Illumina SNP array, genotyping-by-sequencing, or DArTseq platforms) and/or multiple gene/QTL region-specific molecular markers (using KASP platform). All genotyped samples are registered in the "DNA SampleTracker," a software system for tracking DNA samples developed at CIMMYT. In collaboration with High Throughput Genotyping Platform project, the plant sample and data collection methods are optimized. Meanwhile, the extensive wheat genealogies and phenotypic information have been maintained in the International Wheat Information System and will be transferred to a new Enterprise Breeding System. Furthermore, several bioinformatics/statistical genetics methods with the objectives of gene discovery and genomic prediction have been developed and utilized for optimizing genomics-assisted selection. The wheat team is a member of "Genomic Open-source Breeding Informatics Initiative (GOBII)" which aims to develop and implement genomic data management systems to enhance the capacity of breeding programs. Under this initiative, a new genomics database has been built and a pilot wheat version is being tested at CIMMYT. Several decision support tools are also under collaborative development, such as a Genomic Selection Pipeline based on Galaxy, Flapjack-based F1/line verification, and marker assisted backcrossing tools. Additional tools are envisioned for the future including a Cross-Assistor and Selection-Assistor. The ultimate aim is to seamlessly connect the genomic database, phenotypic database, and decision support tools to support the breeding selection process and to lead to the development of cultivars with increased rates of genetic gain.

Rust diseases in wheat are the major threat to wheat production and yield gains. The breakdown in resistance of certain major genes and new emerging aggressive races of rusts are causing serious concerns in all main wheat growing areas of the world. Therefore, it is the need of the hour to search for new sources of resistance genes or QTL's for effective utilization in future breeding programs. In total 100 wheat genotypes were evaluated for seedling and adult-plant resistance to stem rust races TKTTF and TTKSK at Tel Hadya-Syria, and Njoro-Kenya, and Kelardasht-Iran. Evaluation to Yr27 virulent stripe rust race was carried out at Tel Hadya and Terbol-Lebanon research stations. In this study we used genome wide association studies (GWAS) to identify markers or QTLs linked to stem rust and stripe rust races using Diversity Arrays Technology (DArT?) in selected 35 Iranian wheat genotypes. The association of markers and phenotypes was carried out using a unified mixed-model approach (MLM) as implemented in the genome association and prediction integrated tool (GAPIT). Out of 3,072 markers, 986 were polymorphic and used for marker trait associations. A total of 44 DArT markers were identified to be significantly (p<=0.01) associated with studied traits in 16 genomic regions 1A, 1B, 2A, 4A, 6A, 7A, 1B.1R, 2B, 3B, 4B, 5B, 5B.7B, 6B, 7D and an unknown region. Among associated markers, 34 were linked to stem and nine to stripe rust. They were found on 16 genomic regions on chromosome arms 1A, 1B, 2A, 4A, 6A, 7A, 1B.1R, 2B, 3B, 4B, 5B, 5B.7B, 6B, 7D and an unknown region. Associated markers explained phenotypic variation ranging from 21 to 65%. In addition to validation of previously identified genes, this study revealed new QTL's linked to stem and stripe rust which will assist breeders to develop new resistant varieties.

Breeding rust resistant cultivars using conventional methods is time-consuming, complex and slow, but molecular markers offer a rapid alternative for developing cultivars with improved disease resistance. Three wheat cultivars, DBW88, DBW107, and DBW110, from different production zones were used as recipients for incorporation of resistance genes using a marker-assisted backcross (MAB) breeding approach. Leaf rust resistance gene Lr32 is being incorporated into all the three varieties, stripe rust resistance gene Yr15 is being incorporated into DBW88 and DBW107, and stem rust resistance gene Sr26 is being added to variety DBW110. Lines PBW703 (Yr15), FLW15 (Lr32) and Avocet (Sr26) were used as donors. Six cross combinations viz., DBW88/PBW703, DBW107/PBW703, DBW88/FLW15, DBW107/FLW15, DBW110/FLW15 and DBW110/Sr26 were made at Karnal during 2015-16 and the crosses were grown at IIWBR-RS, Dalang Maidan for backcrossing. BC1F1 plants were raised at Karnal during 2016-17. Both foreground and background selections were practiced in each combination. SSR markers gwm264 and barc135 were used for foreground selection of Lr32, marker barc8 was used for selection of Yr15, and markers Sr26#43 and BE518379 were used to detect presence and absence of Sr26. From 90 to 127 polymorphic SSR markers chosen for each cross from an initial set of 800 screened on the parents are being used for background selection.

The Cereal Crops Research Institute (CCRI) is situated on the left bank of River Kabul, near village Pirsabak, 3 km east of Nowshera at an elevation of 288 m above sea level on the intersection of 74? E longitude and 32? N latitude. In July 2010, a devastating flood destroyed all the available germplasm, machineries, laboratories, and field equipment. After the flood research activities were restarted with full motivation, dedication and hard work in collaboration with PARC, ICARDA, CIMMYT, and with the help of wheat productivity enhancement program (WPEP). Developed new population of wheat via spring x spring, spring x facultative germplasm to elevate genetic diversity and lines selected from segregating populations for high yield and rust resistance are at advanced stage of testing.

Since the flood, the CCRI developed four new wheat cultivars: Pirsabak-2013 Pakhtunkhwa-2015 for irrigated areas and Shahkar-2013 and Pirsabak-2015 for rainfed areas of Khyber Pakhtunkhwa, Pakistan. Varietal maintenance and seed production of the released varieties has been undertaken by the wheat breeding team effectively. The seed of these newly developed wheat cultivars was multiplied on fast track basis through pre-released seed multiplication and now these four varieties are the most popular cultivars of Khyber Pakhtunkhwa, Pakistan. Three new candidate wheat lines (PR-106, PR-110 and PR-112) have been submitted to provincial seed council for approval as new wheat cultivars for Khyber Pakhtunkhwa, Pakistan. Two new candidate lines i.e. PR-115 and PR-118 got first position in National Uniform Wheat Yield Trials (NUWYT) on the basis of grain yield during 2016-17 under irrigated and rainfed conditions, respectively.